bit-package: A class for vectors of 1-bit booleans

In OHDSI/bit: A Class for Vectors of 1-Bit Booleans

Description

Package 'bit' provides bitmapped vectors of booleans (no NAs), coercion from and to logicals, integers and integer subscripts; fast boolean operators and fast summary statistics.

With bit vectors you can store true binary booleans {FALSE,TRUE} at the expense of 1 bit only, on a 32 bit architecture this means factor 32 less RAM and factor 32 more speed on boolean operations. With this speed gain it even pays-off to convert to bit in order to avoid a single boolean operation on logicals or a single set operation on (longer) integer subscripts, the pay-off is dramatic when such components are used more than once.

Reading from and writing to bit is approximately as fast as accessing standard logicals - mostly due to R's time for memory allocation. The package allows to work with pre-allocated memory for return values by calling .Call() directly: when evaluating the speed of C-access with pre-allocated vector memory, coping from bit to logical requires only 70% of the time for copying from logical to logical; and copying from logical to bit comes at a performance penalty of 150%.

Since bit objects cannot be used as subsripts in R, a second class 'bitwhich' allows to store selections as efficiently as possible with standard R types. This is usefull either to represent parts of bit objects or to represent very asymetric selections.

Class 'ri' (range index) allows to select ranges of positions for chunked processing: all three classes 'bit', 'bitwhich' and 'ri' can be used for subsetting 'ff' objects (ff-2.1.0 and higher).

Usage

 bit(length)
 ## S3 method for class 'bit'
print(x, ...)

Arguments

length	length of vector in bits
x	a bit vector
...	further arguments to print

Details

Package:	bit
Type:	Package
Version:	1.1.0
Date:	2012-06-05
License:	GPL-2
LazyLoad:	yes
Encoding:	latin1

Index:

bit function	bitwhich function	ri function	see also	description
.BITS			globalenv	variable holding number of bits on this system
bit_init			.First.lib	initially allocate bit-masks (done in .First.lib)
bit_done			.Last.lib	finally de-allocate bit-masks (done in .Last.lib)
bit	bitwhich	ri	logical	create bit object
print.bit	print.bitwhich	print.ri	print	print bit vector
length.bit	length.bitwhich	length.ri	length	get length of bit vector
length<-.bit	length<-.bitwhich		length<-	change length of bit vector
c.bit	c.bitwhich		c	concatenate bit vectors
is.bit	is.bitwhich	is.ri	is.logical	test for bit class
as.bit	as.bitwhich		as.logical	generically coerce to bit or bitwhich
as.bit.logical	as.bitwhich.logical		logical	coerce logical to bit vector (FALSE => FALSE, c(NA, TRUE) => TRUE)
as.bit.integer	as.bitwhich.integer		integer	coerce integer to bit vector (0 => FALSE, ELSE => TRUE)
as.bit.double	as.bitwhich.double		double	coerce double to bit vector (0 => FALSE, ELSE => TRUE)
as.double.bit	as.double.bitwhich	as.double.ri	as.double	coerce bit vector to double (0/1)
as.integer.bit	as.integer.bitwhich	as.integer.ri	as.integer	coerce bit vector to integer (0L/1L)
as.logical.bit	as.logical.bitwhich	as.logical.ri	as.logical	coerce bit vector to logical (FALSE/TRUE)
as.which.bit	as.which.bitwhich	as.which.ri	as.which	coerce bit vector to positive integer subscripts
as.bit.which	as.bitwhich.which		bitwhich	coerce integer subscripts to bit vector
as.bit.bitwhich	as.bitwhich.bitwhich			coerce from bitwhich
as.bit.bit	as.bitwhich.bit		UseMethod	coerce from bit
as.bit.ri	as.bitwhich.ri			coerce from range index
as.bit.ff			ff	coerce ff boolean to bit vector
as.ff.bit			as.ff	coerce bit vector to ff boolean
as.hi.bit	as.hi.bitwhich	as.hi.ri	as.hi	coerce to hybrid index (requires package ff)
as.bit.hi	as.bitwhich.hi			coerce from hybrid index (requires package ff)
[[.bit			[[	get single bit (index checked)
[[<-.bit			[[<-	set single bit (index checked)
[.bit			[	get vector of bits (unchecked)
[<-.bit			[<-	set vector of bits (unchecked)
!.bit	!.bitwhich	(works as second arg in	!	boolean NOT on bit
&.bit	&.bitwhich	bit and bitwhich ops)	&	boolean AND on bit
|.bit	|.bitwhich		|	boolean OR on bit
xor.bit	xor.bitwhich		xor	boolean XOR on bit
!=.bit	!=.bitwhich		!=	boolean unequality (same as XOR)
==.bit	==.bitwhich		==	boolean equality
all.bit	all.bitwhich	all.ri	all	aggregate AND
any.bit	any.bitwhich	any.ri	any	aggregate OR
min.bit	min.bitwhich	min.ri	min	aggregate MIN (first TRUE position)
max.bit	max.bitwhich	max.ri	max	aggregate MAX (last TRUE position)
range.bit	range.bitwhich	range.ri	range	aggregate [MIN,MAX]
sum.bit	sum.bitwhich	sum.ri	sum	aggregate SUM (count of TRUE)
summary.bit	summary.bitwhich	summary.ri	tabulate	aggregate c(nFALSE, nTRUE, minRange, maxRange)
regtest.bit				regressiontests for the package

Value

bit returns a vector of integer sufficiently long to store 'length' bits (but not longer) with an attribute 'n' and class 'bit'

Note

Currently operations on bit objects have some overhead from R-calls. Do expect speed gains for vectors of length ~ 10000 or longer.
Since this package was created for high performance purposes, only positive integer subscripts are allowed: All R-functions behave as expected - i.e. they do not change their arguments and create new return values. If you want to save the time for return value memory allocation, you must use .Call directly (see the dontrun example in sum.bit).

Author(s)

Jens Oehlschlägel <[e-mail]>

Maintainer: Jens Oehlschlägel <[e-mail]>

See Also

logical in base R and vmode in package 'ff'

Examples

  x <- bit(12)                                 # create bit vector
  x                                            # autoprint bit vector
  length(x) <- 16                              # change length
  length(x)                                    # get length
  x[[2]]                                       # extract single element
  x[[2]] <- TRUE                               # replace single element
  x[1:2]                                       # extract parts of bit vector
  x[1:2] <- TRUE                               # replace parts of bit vector
  as.which(x)                                  # coerce bit to subscripts
  x <- as.bit.which(3:4, 4)                    # coerce subscripts to bit
  as.logical(x)                                # coerce bit to logical
  y <- as.bit(c(FALSE, TRUE, FALSE, TRUE))     # coerce logical to bit
  is.bit(y)                                    # test for bit
  !x                                           # boolean NOT
  x & y                                        # boolean AND
  x | y                                        # boolean OR
  xor(x, y)                                    # boolean Exclusive OR
  x != y                                       # boolean unequality (same as xor)
  x == y                                       # boolean equality
  all(x)                                       # aggregate AND
  any(x)                                       # aggregate OR
  min(x)                                       # aggregate MIN (integer version of ALL)
  max(x)                                       # aggregate MAX (integer version of ANY)
  range(x)                                     # aggregate [MIN,MAX]
  sum(x)                                       # aggregate SUM (count of TRUE)
  summary(x)                                   # aggregate count of FALSE and TRUE

  ## Not run: 
    message("\nEven for a single boolean operation transforming logical to bit pays off")
    n <- 10000000
    x <- sample(c(FALSE, TRUE), n, TRUE)
    y <- sample(c(FALSE, TRUE), n, TRUE)
    system.time(x|y)
    system.time({
       x <- as.bit(x)
       y <- as.bit(y)
    })
    system.time( z <- x | y )
    system.time( as.logical(z) )
    message("Even more so if multiple operations are needed :-)")

    message("\nEven for a single set operation transforming subscripts to bit pays off\n")
    n <- 10000000
    x <- sample(n, n/2)
    y <- sample(n, n/2)
    system.time( union(x,y) )
    system.time({
     x <- as.bit.which(x, n)
     y <- as.bit.which(y, n)
    })
    system.time( as.which.bit( x | y ) )
    message("Even more so if multiple operations are needed :-)")

    message("\nSome timings WITH memory allocation")
    n <- 2000000
    l <- sample(c(FALSE, TRUE), n, TRUE)
    # copy logical to logical
    system.time(for(i in 1:100){  # 0.0112
       l2 <- l
       l2[1] <- TRUE   # force new memory allocation (copy on modify)
       rm(l2)
    })/100
    # copy logical to bit
    system.time(for(i in 1:100){  # 0.0123
       b <- as.bit(l)
       rm(b)
    })/100
    # copy bit to logical
    b <- as.bit(l)
    system.time(for(i in 1:100){  # 0.009
       l2 <- as.logical(b)
       rm(l2)
    })/100
    # copy bit to bit
    b <- as.bit(l)
    system.time(for(i in 1:100){  # 0.009
       b2 <- b
       b2[1] <- TRUE   # force new memory allocation (copy on modify)
       rm(b2)
    })/100


    l2 <- l
    # replace logical by TRUE
    system.time(for(i in 1:100){
       l[] <- TRUE
    })/100
    # replace bit by TRUE (NOTE that we recycle the assignment  
		 # value on R side == memory allocation and assignment first)
    system.time(for(i in 1:100){
       b[] <- TRUE
    })/100
    # THUS the following is faster
    system.time(for(i in 1:100){
       b <- !bit(n)
    })/100

    # replace logical by logical
    system.time(for(i in 1:100){
       l[] <- l2
    })/100
    # replace bit by logical
    system.time(for(i in 1:100){
       b[] <- l2
    })/100
    # extract logical
    system.time(for(i in 1:100){
       l2[]
    })/100
    # extract bit
    system.time(for(i in 1:100){
       b[]
    })/100

    message("\nSome timings WITHOUT memory allocation (Serge, that's for you)")
    n <- 2000000L
    l <- sample(c(FALSE, TRUE), n, TRUE)
    b <- as.bit(l)
    # read from logical, write to logical
    l2 <- logical(n)
    system.time(for(i in 1:100).Call("R_filter_getset", l, l2, PACKAGE="bit")) / 100
    # read from bit, write to logical
    l2 <- logical(n)
    system.time(for(i in 1:100).Call("R_bit_get", b, l2, c(1L, n), PACKAGE="bit")) / 100
    # read from logical, write to bit
    system.time(for(i in 1:100).Call("R_bit_set", b, l2, c(1L, n), PACKAGE="bit")) / 100

  
## End(Not run)

OHDSI/bit documentation built on May 7, 2019, 8:30 p.m.